So I've been thinking about this topic for a little while and I came to realise that a lot of the changes I'd propose don't actually affect the storyline directly. Instead, they're the details and mechanics that could have enriched gameplay for me, and the overall experience of the game. For example, I'd have liked to see the gang territory mechanic used in such a way that felt more varied, and wasn't dropped a few missions following the introduction of it. It barely feels like we've had time to play around with it before we're whisked away into the countryside. Having more variety in the gang attacks too would be nice, but again it doesn't really change the story. I know they're a key part to the post-game (with us having to acquire a certain number of territories before we can progress) but I wouldn't consider that a storyline change. That to me would be a mechanic change.
I think there's a lot of divide over the more OTT missions, particularly the ones involving The Truth and Toreno. In my opinion, both characters are great and add a good deal of variety to the game - like it or not, flying planes across the bay and stealing alien artefacts is a far cry from the hood-rat scene you started with in Los Santos. Bet you didn't see that coming! While it would be nice to see a change in these mission strands, I think I'm saying that because I've played the game to death and I'd love to see more of the same, not so much because I think the story is bad. Instead of stealing green goo from a flatbed train for no reason, have us dabble in more of the conspiracies that float around The Truth's head. We can still use the new environment offered to us. How about following a leaker from the Lil' Probe Inn to see what he's hiding and where? Or an assassination attempt on Toreno that echoes back to saving Love Fist from the deranged stalker back in Vice City? Again, I'm only suggesting these missions as additions, and not so much as replacements... well, maybe replace the green goo one. I never did care for that.
The casino strand is all well and good to me. It's a little sudden, but it's an exaggeration of knowing the right people. Carl did good work for Woozie, so it stands to reason he would be recommended for such skilled work. Playing the two against each other is fun too, and it added a degree of tension doing work for both families knowing where our loyalties really lied.